OTL France successfully assimilated the Alsatians to a great extent through offering them political liberty and treating them as Frenchmen, as opposed to Imperial Germany which treated them as conquered subjects and not as Germans. I would argue that the Rhineland could quite possibly have been assimilated in exactly the same way, especially if the anti-revolutionary powers of Europe, in reaction against the continued existence of Revolutionary France, were even more reactionary than in OTL.
That is exactly the problem I'm referring to. They're going to get assimilated into France and their birth rates are going to fall as a result; the adoption of contraceptives and control over childbearing tends to go along cultural and lingual lines in the early adopting societies, at least from the yale series I had watched on the subject (where they had referred to the case of Belgium and Spain, where they spread along the linguists map). France successfully integrating those regions will cause their birth rates and population growth to fall, in all probability. Of course they will be assimilated into France too, but that is only the assimilation of territory, and not demographics itself.
The absolutely tremendous casualties of the Napoleonic Wars—vastly disproportionately consisting of one gender, which of course made it worse—due to Bonaparte conscripting practically every young man who could pick up a rifle and sending them off to die for his insatiable ambitions can be blamed squarely on him. There may well have been a falling birthrate without him anyway, that's absolutely a fair point, but not killing ~10% of the men in France for Bonaparte's ambition would have helped an awful lot.
Demographic impacts of population imbalance are long lasting, but one can compare states that took tremendous casualties during the period to France. According to wikipedia Spain took 500,000 casualties, which is some 5%! of their population of around 10m, and yet over the next ~140 years they had a growth rate of 250%. Portugal's losses were even more severe, at 200,000 out of a population of 3m, or circa 6.6%, and yet they grew from 3m to 7.7m. The British had 300,000 out of 10.5m, again according to wikipedia, and yet their population near quintupled from 10.5m to 48m. These were states that all took heavy casualties, even if not on the scale of France (and in the case of Spain/Portugal it was probably somewhat more spread across the genders due to the nature of the fighting there, but I'd still imagine it would be primarily concentrated in the male sector of the population), but their population recovered from it. France didn't, which leads me to the conclusion that while losses from the war are an important factor, and after all can only be partially (albeit that partial nature is the majority, by a large factor) be related to Napoleon, Napoleon himself can't be held to account for the long nature of French demographic problems.
The Republic may well have fought wars, but I doubt that it would have ever done things like the Peninsular War or the invasion of Russia, and after enough French victories the powers of Europe could have settled down with the Republic; they never could with Bonaparte in charge because he was so utterly incapable of any rapprochement with other European powers that didn't consist of "you do exactly what I say".
There aren't really accurate casualties on the various coalitions, so it is hard to look at the First/Second coalitions. There was also of course internal disturbances such as in the Vendee. What is in addition, to stop at least some more wars from popping up between France and enemies? Even if every statement in regard to Napoleon is true on your account (I'm not arguing one way or another), the people who lead the Republic in his absence will not automatically be brilliant statesmen. It is easily possible that additional wars could happen before it is completely proven that the French cannot be dislodged from their position, and additional casualties are going to be sustained from that.
Not to mention that while Napoleon may not be leader, there may be somebody else who shares at least some similar traits. The Directorate wasn't exactly the ideal government after all.